期刊
BMC BIOINFORMATICS
卷 16, 期 -, 页码 -出版社
BMC
DOI: 10.1186/1471-2105-16-S1-S2
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资金
- National Science Council [102-2311-B-009-001, 103-2221-E-009-128-MY2]
- National Chiao Tung University and Ministry of Education (Junior Faculty Research Enhancement Project and Aiming for the Top University Program) of Taiwan
Background: In modern paired-end sequencing protocols short DNA fragments lead to adapter-appended reads. Current paired-end adapter removal approaches trim adapter by scanning the fragment of adapter on the 3' end of the reads, which are not competent in some applications. Results: Here, we propose a fast and highly accurate adapter-trimming algorithm, PEAT, designed specifically for paired-end sequencing. PEAT requires no a priori adaptor sequence, which is convenient for large-scale meta-analyses. We assessed the performance of PEAT with many adapter trimmers in both simulated and real life paired-end sequencing libraries. The importance of adapter trimming was exemplified by the influence of the downstream analyses on RNA-seq, ChIP-seq and MNase-seq. Several useful guidelines of applying adapter trimmers with aligners were suggested. Conclusions: PEAT can be easily included in the routine paired-end sequencing pipeline. The executable binaries and the standalone C++ source code package of PEAT are freely available online.
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